This series of files compile analyses done for the specific analysis of Chapter 1, for the regional campaign of 2017.

All analyses have been done with PRIMER-e 6 and R 4.0.2.

Click on the table of contents in the left margin to assess a specific analysis.
Click on a figure to zoom it

We used data from subtidal ecosystems (see metadata files for more information). Only stations that have been sampled both for abiotic parameters and benthic species were included.

Selected variables for the analyses:

Depth of the station: depth (only for ANCOVAs)
Percentage of organic matter: om
Percentage of gravel: gravel
Percentage of sand: sand
Percentage of silt: silt
Percentage of clay: clay
Concentration of arsenic: arsenic
Concentration of cadmium: cadmium
Concentration of chromium: chromium
Concentration of copper: copper
Concentration of iron: iron
Concentration of manganese: manganese
Concentration of mercury: mercury
Concentration of lead: lead
Concentration of zinc: zinc
Specific richness: S(only for 500 µm communities)
Total density of individuals: N (only for 500 µm communities)
Shannon’s diversity: H (only for 500 µm communities)
Piélou’s evenness: J (only for 500 µm communities)

We only considered 500 µm communities for these analyses. Abundances of Bipalponephtys neotena (Bneo) and Nematoda (Nema) were also considered (see IndVal and SIMPER results).

Heavy metal concentrations for campaign 2017 have been kriged from the values collected at campaigns 2014 and 2016. As data is missing for metal concentrations outside BSI, two Designs have been used:

Design 1: stations at BSI, MR with habitat parameters
Design 2: stations at BSI with heavy metal concentrations.

Statistics for each variable considered:

	Mean	SD	SE	Median	Min	Max	95% CI
depth	20.879	20.410	4.166	13.600	1.600	66.900	8.166
om	1.121	0.813	0.166	0.925	0.289	3.872	0.325
gravel	0.007	0.027	0.006	0.000	0.000	0.130	0.011
sand	0.596	0.216	0.044	0.546	0.131	0.970	0.087
silt	0.397	0.225	0.046	0.454	0.030	0.869	0.090
clay	0.000	0.000	0.000	0.000	0.000	0.000	0.000
S_500	10.917	5.656	1.155	10.500	1.000	23.000	2.263
N_500	95.917	95.382	19.470	70.500	1.000	382.000	38.160
H_500	1.572	0.685	0.140	1.576	0.000	2.568	0.274
J_500	0.683	0.243	0.050	0.689	0.000	1.000	0.097
arsenic	3.908	3.085	0.630	2.750	1.500	16.000	1.234
cadmium	0.150	0.041	0.008	0.145	0.090	0.230	0.017
chromium	55.163	20.949	4.276	54.750	28.000	110.700	8.381
copper	11.121	6.686	1.365	8.950	2.900	28.700	2.675
iron	49908.033	13633.036	2782.832	48883.150	28355.900	78471.300	5454.250
manganese	952.654	455.270	92.932	847.700	423.100	2098.000	182.142
mercury	0.024	0.016	0.003	0.021	0.008	0.087	0.006
lead	5.533	2.520	0.514	5.050	2.400	12.100	1.008
zinc	61.654	25.066	5.117	55.750	33.500	141.000	10.028

	Mean	SD	SE	Median	Min	Max	95% CI
depth	24.740	14.201	3.667	24.600	3.300	52.000	7.187
om	0.507	0.311	0.080	0.389	0.186	1.334	0.157
gravel	0.061	0.182	0.047	0.000	0.000	0.701	0.092
sand	0.734	0.331	0.085	0.875	0.005	0.992	0.167
silt	0.154	0.180	0.046	0.074	0.007	0.587	0.091
clay	0.051	0.133	0.034	0.000	0.000	0.407	0.067
S_500	9.667	3.754	0.969	11.000	3.000	16.000	1.900
N_500	54.000	37.558	9.697	39.000	14.000	118.000	19.006
H_500	1.614	0.520	0.134	1.659	0.509	2.241	0.263
J_500	0.729	0.148	0.038	0.746	0.461	0.939	0.075

1. Maps

1.1. General map

1.2. Parameters maps

For maps of heavy metal concentrations, stations have been grouped based on Environment Canada (2007) classification of sediment toxicity (grey = low toxicity, red = high toxicity).

OM

Gravel

Sand

Silt

Clay

Arsenic

Cadmium

Chromium

Copper

Iron

Manganese

Mercury

Lead

Zinc

Species

Richness

Density

Diversity

Evenness

2. Figures

2.1. Barplots

Two types of barplots are available: one for the means by region, and one for the means by depth class. The latter have been done by classifying stations along three groups, based on their depth: shallow (0-10 m), medium (10-25 m) and deep (> 25 m). These thresholds are not supported by evidence, but allow to get a balanced design (26 stations for each depth class). However, we have been using PERMANOVA with depth as a covariate, instead of using these classes as a third factor.

Heavy metals are not presented here, as they were only sampled at BSI stations.

Regions

Organic matter

Grain-size

Species abundances

Diversity indices

Depth classes

Organic matter

Grain-size

Species abundances

Diversity indices

2.2. Phylum frequencies

Phylum abundances by condition
Phylum	HI	R
Arthropoda	879	81
Annelida	811	40
Mollusca	337	310
Nematoda	242	270
Echinodermata	29	104
Nemertea	4	0
Bryozoa	0	0
Chaetognatha	0	0
Cnidaria	0	3
Hemichordata	0	0
Phoronida	0	0
Platyhelminthes	0	0
Sipuncula	0	2